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Volumn 118, Issue 7, 2014, Pages 1799-1812

Computing stability effects of mutations in human superoxide dismutase 1

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DIMERS; MOLECULAR BIOLOGY; MONOMERS; OXYGEN; PROTEINS;

EID: 84894567297     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp4119138     Document Type: Article
Times cited : (28)

References (51)
  • 2
    • 80053047560 scopus 로고    scopus 로고
    • Correlating Disease-Related Mutations to Their Effect on Protein Stability: A Large-Scale Analysis of the Human Proteome
    • Casadio, R.; Vassura, M.; Tiwari, S.; Fariselli, P.; Martelli, P. L. Correlating Disease-Related Mutations to Their Effect on Protein Stability: A Large-Scale Analysis of the Human Proteome Hum. Mutat. 2011, 32, 1161-1170
    • (2011) Hum. Mutat. , vol.32 , pp. 1161-1170
    • Casadio, R.1    Vassura, M.2    Tiwari, S.3    Fariselli, P.4    Martelli, P.L.5
  • 3
    • 77954743785 scopus 로고    scopus 로고
    • Mutational Effects and the Evolution of New Protein Functions
    • Soskine, M.; Tawfik, D. S. Mutational Effects and the Evolution of New Protein Functions Nat. Rev. Genet. 2010, 11, 572-582
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 572-582
    • Soskine, M.1    Tawfik, D.S.2
  • 4
    • 41949103740 scopus 로고    scopus 로고
    • The Structure of Protein Evolution and the Evolution of Protein Structure
    • Goldstein, R. A. The Structure of Protein Evolution and the Evolution of Protein Structure Curr. Opin. Struct. Biol. 2008, 18, 170-177
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 170-177
    • Goldstein, R.A.1
  • 5
    • 84865730325 scopus 로고    scopus 로고
    • Protein Biophysics Explains Why Highly Abundant Proteins Evolve Slowly
    • Serohijos, A. W. R.; Rimas, Z.; Shakhnovich, E. I. Protein Biophysics Explains Why Highly Abundant Proteins Evolve Slowly Cell 2012, 2, 249-256
    • (2012) Cell , vol.2 , pp. 249-256
    • Serohijos, A.W.R.1    Rimas, Z.2    Shakhnovich, E.I.3
  • 7
    • 80052659359 scopus 로고    scopus 로고
    • Bridging the Gap between Chemistry, Physiology, and Evolution: Quantifying the Functionality of Sperm Whale Myoglobin Mutants
    • Dasmeh, P.; Kepp, K. P. Bridging the Gap between Chemistry, Physiology, and Evolution: Quantifying the Functionality of Sperm Whale Myoglobin Mutants Comp. Biochem. Physiol., Part A: Mol. Integr. Physiol. 2012, 161, 9-17
    • (2012) Comp. Biochem. Physiol., Part A: Mol. Integr. Physiol. , vol.161 , pp. 9-17
    • Dasmeh, P.1    Kepp, K.P.2
  • 8
    • 84875986323 scopus 로고    scopus 로고
    • Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability
    • Dasmeh, P.; Serohijos, A.; Kepp, K. P.; Shakhnovich, E. I. Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability PLoS Comput. Biol. 2013, 9 e1002929
    • (2013) PLoS Comput. Biol. , vol.9
    • Dasmeh, P.1    Serohijos, A.2    Kepp, K.P.3    Shakhnovich, E.I.4
  • 10
    • 0346034910 scopus 로고    scopus 로고
    • Production of Reactive Oxygen Species by Isolated Mitochondria of the Antarctic Bivalve Laternula Elliptica (King and Broderip) under Heat Stress
    • Heise, K.; Puntarulo, S.; Pörtner, H. O.; Abele, D. Production of Reactive Oxygen Species by Isolated Mitochondria of the Antarctic Bivalve Laternula Elliptica (King and Broderip) under Heat Stress Comp. Biochem. Physiol., Part C: Pharmacol., Toxicol. Endocrinol. 2003, 134, 79-90
    • (2003) Comp. Biochem. Physiol., Part C: Pharmacol., Toxicol. Endocrinol. , vol.134 , pp. 79-90
    • Heise, K.1    Puntarulo, S.2    Pörtner, H.O.3    Abele, D.4
  • 11
    • 74449091635 scopus 로고    scopus 로고
    • Superoxide Dismutases - A Review of the Metal-Associated Mechanistic Variations
    • Abreu, I. A.; Cabelli, D. E. Superoxide Dismutases-A Review of the Metal-Associated Mechanistic Variations Biochim. Biophys. Acta 2010, 1804, 263-274
    • (2010) Biochim. Biophys. Acta , vol.1804 , pp. 263-274
    • Abreu, I.A.1    Cabelli, D.E.2
  • 13
    • 84875896727 scopus 로고    scopus 로고
    • Clinical and Genetic Heterogeneity of Amyotrophic Lateral Sclerosis
    • Sabatelli, M.; Conte, A.; Zollino, M. Clinical and Genetic Heterogeneity of Amyotrophic Lateral Sclerosis Clin. Genet. 2013, 83, 408-416
    • (2013) Clin. Genet. , vol.83 , pp. 408-416
    • Sabatelli, M.1    Conte, A.2    Zollino, M.3
  • 17
    • 20444504724 scopus 로고    scopus 로고
    • Amyotrophic Lateral Sclerosis Mutations have the Greatest Destabilizing Effect on the Apo- and Reduced Form of SOD1, Leading to Unfolding and Oxidative Aggregation
    • Furukawa, Y.; O'Halloran, T. V. Amyotrophic Lateral Sclerosis Mutations have the Greatest Destabilizing Effect on the Apo- and Reduced Form of SOD1, Leading to Unfolding and Oxidative Aggregation J. Biol. Chem. 2005, 280, 17266-17274
    • (2005) J. Biol. Chem. , vol.280 , pp. 17266-17274
    • Furukawa, Y.1    O'Halloran, T.V.2
  • 18
    • 80051791216 scopus 로고    scopus 로고
    • Biochemical Properties and in Vivo Effects of the SOD1 Zinc-Binding Site Mutant (H80G)
    • Son, M.; Srikanth, U.; Puttaparthi, K.; Luther, C.; Elliott, J. L. Biochemical Properties and in Vivo Effects of the SOD1 Zinc-Binding Site Mutant (H80G) J. Neurochem. 2011, 118, 891-901
    • (2011) J. Neurochem. , vol.118 , pp. 891-901
    • Son, M.1    Srikanth, U.2    Puttaparthi, K.3    Luther, C.4    Elliott, J.L.5
  • 20
    • 79953848210 scopus 로고    scopus 로고
    • Structural and Thermodynamic Effects of Post-Translational Modifications in Mutant and Wild Type Cu, Zn Superoxide Dismutase
    • Proctor, E. A.; Ding, F.; Dokholyan, N. V. Structural and Thermodynamic Effects of Post-Translational Modifications in Mutant and Wild Type Cu, Zn Superoxide Dismutase J. Mol. Biol. 2011, 408, 555-567
    • (2011) J. Mol. Biol. , vol.408 , pp. 555-567
    • Proctor, E.A.1    Ding, F.2    Dokholyan, N.V.3
  • 21
    • 0037013264 scopus 로고    scopus 로고
    • Decreased Metallation and Activity in Subsets of Mutant Superoxide Dismutases Associated with Familial Amyotrophic Lateral Sclerosis
    • Hayward, L. J.; Rodriguez, J. A.; Kim, J. W.; Tiwari, A.; Goto, J. J.; Cabelli, D. E.; Valentine, J. S.; Brown, R. H., Jr. Decreased Metallation and Activity in Subsets of Mutant Superoxide Dismutases Associated with Familial Amyotrophic Lateral Sclerosis J. Biol. Chem. 2002, 277, 15923-15931
    • (2002) J. Biol. Chem. , vol.277 , pp. 15923-15931
    • Hayward, L.J.1    Rodriguez, J.A.2    Kim, J.W.3    Tiwari, A.4    Goto, J.J.5    Cabelli, D.E.6    Valentine, J.S.7    Brown, Jr.R.H.8
  • 22
    • 80051503291 scopus 로고    scopus 로고
    • Glutathionylation at Cys-111 Induces Dissociation of Wild Type and FALS Mutant SOD1 Dimers
    • Redler, R. L.; Wilcox, K. C.; Proctor, E. A.; Fee, L.; Caplow, M.; Dokholyan, N. V. Glutathionylation at Cys-111 Induces Dissociation of Wild Type and FALS Mutant SOD1 Dimers Biochemistry 2011, 50, 7057-7066
    • (2011) Biochemistry , vol.50 , pp. 7057-7066
    • Redler, R.L.1    Wilcox, K.C.2    Proctor, E.A.3    Fee, L.4    Caplow, M.5    Dokholyan, N.V.6
  • 23
    • 74549207309 scopus 로고    scopus 로고
    • Assessing Computational Methods for Predicting Protein Stability upon Mutation: Good on Average but Not in the Details
    • Potapov, V.; Cohen, M.; Schreiber, G. Assessing Computational Methods for Predicting Protein Stability upon Mutation: Good on Average but Not in the Details Protein Eng., Des. Sel. 2009, 22, 553-560
    • (2009) Protein Eng., Des. Sel. , vol.22 , pp. 553-560
    • Potapov, V.1    Cohen, M.2    Schreiber, G.3
  • 24
    • 14144256681 scopus 로고    scopus 로고
    • Energy Functions for Protein Design: Adjustment with Protein-Protein Complex Affinities, Models for the Unfolded State, and Negative Design of Solubility and Specificity
    • Pokala, N.; Handel, T. M. Energy Functions for Protein Design: Adjustment with Protein-Protein Complex Affinities, Models for the Unfolded State, and Negative Design of Solubility and Specificity J. Mol. Biol. 2005, 347, 203-227
    • (2005) J. Mol. Biol. , vol.347 , pp. 203-227
    • Pokala, N.1    Handel, T.M.2
  • 25
    • 23144461249 scopus 로고    scopus 로고
    • I-Mutant2.0: Predicting Stability Changes upon Mutation from the Protein Sequence or Structure
    • Capriotti, E.; Fariselli, P.; Casadio, R. I-Mutant2.0: Predicting Stability Changes upon Mutation from the Protein Sequence or Structure Nucleic Acids Res. 2005, 33, W306-W310
    • (2005) Nucleic Acids Res. , vol.33
    • Capriotti, E.1    Fariselli, P.2    Casadio, R.3
  • 27
    • 0036291145 scopus 로고    scopus 로고
    • Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of more than 1000 Mutations
    • Guerois, R.; Nielsen, J. E.; Serrano, L. Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of more than 1000 Mutations J. Mol. Biol. 2002, 320, 369-387
    • (2002) J. Mol. Biol. , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 29
    • 77952706843 scopus 로고    scopus 로고
    • Performance of Protein Stability Predictors
    • Khan, S.; Vihinen, M. Performance of Protein Stability Predictors Hum. Mutat. 2010, 31, 675-684
    • (2010) Hum. Mutat. , vol.31 , pp. 675-684
    • Khan, S.1    Vihinen, M.2
  • 30
    • 34248674895 scopus 로고    scopus 로고
    • The Stability Effects of Protein Mutations Appear to be Universally Distributed
    • Tokuriki, N.; Stricher, F.; Schymkowitz, J.; Serrano, L.; Tawfik, D. S. The Stability Effects of Protein Mutations Appear to be Universally Distributed J. Mol. Biol. 2007, 369, 1318-1332
    • (2007) J. Mol. Biol. , vol.369 , pp. 1318-1332
    • Tokuriki, N.1    Stricher, F.2    Schymkowitz, J.3    Serrano, L.4    Tawfik, D.S.5
  • 31
    • 79959942908 scopus 로고    scopus 로고
    • SDM - A Server for Predicting Effects of Mutations on Protein Stability and Malfunction
    • Worth, C. L.; Preissner, R.; Blundell, T. L. SDM-A Server for Predicting Effects of Mutations on Protein Stability and Malfunction Nucleic Acids Res. 2011, 39, W215-W222
    • (2011) Nucleic Acids Res. , vol.39
    • Worth, C.L.1    Preissner, R.2    Blundell, T.L.3
  • 32
    • 0034460414 scopus 로고    scopus 로고
    • PoPMuSiC, an Algorithm for Predicting Protein Mutant Stability Changes: Application to Prion Proteins
    • Gilis, D.; Rooman, M. PoPMuSiC, an Algorithm for Predicting Protein Mutant Stability Changes: Application to Prion Proteins Protein Eng. 2000, 13, 849-856
    • (2000) Protein Eng. , vol.13 , pp. 849-856
    • Gilis, D.1    Rooman, M.2
  • 33
    • 0036948069 scopus 로고    scopus 로고
    • PoPMuSiC, Rationally Designing Point Mutations in Protein Structures
    • Kwasigroch, J. M.; Gilis, D.; Dehouck, Y.; Rooman, M. PoPMuSiC, Rationally Designing Point Mutations in Protein Structures Bioinformatics 2002, 18, 1701-1702
    • (2002) Bioinformatics , vol.18 , pp. 1701-1702
    • Kwasigroch, J.M.1    Gilis, D.2    Dehouck, Y.3    Rooman, M.4
  • 34
    • 84864555615 scopus 로고    scopus 로고
    • Structure-Based Mutant Stability Predictions on Proteins of Unknown Structure
    • Gonnelli, G.; Rooman, M.; Dehouck, Y. Structure-Based Mutant Stability Predictions on Proteins of Unknown Structure J. Biotechnol. 2012, 161, 287-293
    • (2012) J. Biotechnol. , vol.161 , pp. 287-293
    • Gonnelli, G.1    Rooman, M.2    Dehouck, Y.3
  • 35
    • 37749052245 scopus 로고    scopus 로고
    • Prediction of Protein Stability upon Point Mutations
    • Gromiha, M. M. Prediction of Protein Stability upon Point Mutations Biochem. Soc. Trans. 2007, 35, 1569-1573
    • (2007) Biochem. Soc. Trans. , vol.35 , pp. 1569-1573
    • Gromiha, M.M.1
  • 36
    • 33747838537 scopus 로고    scopus 로고
    • CUPSAT: Prediction of Protein Stability upon Point Mutations
    • Partiban, V.; Gromiha, M. M.; Schomburg, D. CUPSAT: Prediction of Protein Stability upon Point Mutations Nucleic Acids Res. 2006, 34, W239-W242
    • (2006) Nucleic Acids Res. , vol.34
    • Partiban, V.1    Gromiha, M.M.2    Schomburg, D.3
  • 37
    • 84870051131 scopus 로고    scopus 로고
    • Accurate Stabilities of Laccase Mutants Predicted with a Modified FoldX Protocol
    • Christensen, N. J.; Kepp, K. P. Accurate Stabilities of Laccase Mutants Predicted with a Modified FoldX Protocol J. Chem. Inf. Model. 2012, 52, 3028-3042
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 3028-3042
    • Christensen, N.J.1    Kepp, K.P.2
  • 38
    • 84880023622 scopus 로고    scopus 로고
    • Stability Mechanisms of Laccase Isoforms using a Modified FoldX Protocol Applicable to Widely Different Proteins
    • Christensen, N. J.; Kepp, K. P. Stability Mechanisms of Laccase Isoforms using a Modified FoldX Protocol Applicable to Widely Different Proteins J. Chem. Theory Comput. 2013, 9, 3210-3223
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3210-3223
    • Christensen, N.J.1    Kepp, K.P.2
  • 39
    • 84868133037 scopus 로고    scopus 로고
    • Assessing Predictors of Changes in Protein Stability upon Mutation using Self-Consistency
    • Thiltgen, G.; Goldstein, R. A. Assessing Predictors of Changes in Protein Stability upon Mutation using Self-Consistency PLoS One 2012, 7 e46084
    • (2012) PLoS One , vol.7
    • Thiltgen, G.1    Goldstein, R.A.2
  • 40
    • 33745889333 scopus 로고    scopus 로고
    • Folding of Cu/Zn Superoxide Dismutase Suggests Structural Hotspots for Gain of Neurotoxic Function in ALS: Parallels to Precursors in Amyloid Disease
    • Nordlund, A.; Oliveberg, M. Folding of Cu/Zn Superoxide Dismutase Suggests Structural Hotspots for Gain of Neurotoxic Function in ALS: Parallels to Precursors in Amyloid Disease Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 10218-10223
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 10218-10223
    • Nordlund, A.1    Oliveberg, M.2
  • 41
    • 22244489417 scopus 로고    scopus 로고
    • Systematically Perturbed Folding Patterns of Amyotrophic Lateral Sclerosis (ALS)-Associated SOD1Mutants
    • Lindberg, M. J.; Byström, R.; Boknäs, N.; Andersen, P. M.; Oliveberg, M. Systematically Perturbed Folding Patterns of Amyotrophic Lateral Sclerosis (ALS)-Associated SOD1Mutants Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 9754-9759
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 9754-9759
    • Lindberg, M.J.1    Byström, R.2    Boknäs, N.3    Andersen, P.M.4    Oliveberg, M.5
  • 42
    • 33646549337 scopus 로고    scopus 로고
    • Calorimetric Analysis of Thermodynamic Stability and Aggregation for Apo and Holo Amyotrophic Lateral Sclerosis-Associated Gly-93 Mutants of Superoxide Dismutase
    • Stathopulos, P. B.; Rumfeldt, J. A.; Karbassi, F.; Siddall, C. A.; Lepock, J. R.; Meiering, E. M. Calorimetric Analysis of Thermodynamic Stability and Aggregation for Apo and Holo Amyotrophic Lateral Sclerosis-Associated Gly-93 Mutants of Superoxide Dismutase J. Biol. Chem. 2006, 281, 6184-6193
    • (2006) J. Biol. Chem. , vol.281 , pp. 6184-6193
    • Stathopulos, P.B.1    Rumfeldt, J.A.2    Karbassi, F.3    Siddall, C.A.4    Lepock, J.R.5    Meiering, E.M.6
  • 43
    • 77953532917 scopus 로고    scopus 로고
    • SOD1Mutations Targeting Surface Hydrogen Bonds Promote Amyotrophic Lateral Sclerosis without Reducing Apo-State Stability
    • Byström, R.; Andersen, P. M.; Gröbner, G.; Oliveberg, M. SOD1Mutations Targeting Surface Hydrogen Bonds Promote Amyotrophic Lateral Sclerosis without Reducing Apo-State Stability J. Biol. Chem. 2010, 285, 19544-19552
    • (2010) J. Biol. Chem. , vol.285 , pp. 19544-19552
    • Byström, R.1    Andersen, P.M.2    Gröbner, G.3    Oliveberg, M.4
  • 44
    • 79955866957 scopus 로고    scopus 로고
    • PoPMuSiC 2.1: A Web Server for the Estimation of Protein Stability Changes upon Mutation and Sequence Optimality
    • Dehouck, Y.; Kwasigroch, J. M.; Gilis, D.; Rooman, M. PoPMuSiC 2.1: A Web Server for the Estimation of Protein Stability Changes upon Mutation and Sequence Optimality BMC Bioinf. 2011, 12, 151
    • (2011) BMC Bioinf. , vol.12 , pp. 151
    • Dehouck, Y.1    Kwasigroch, J.M.2    Gilis, D.3    Rooman, M.4
  • 45
    • 0031023842 scopus 로고    scopus 로고
    • Prediction of the Stability of Protein Mutants Based on Structural Environment-Dependent Amino Acid Substitution and Propensity Tables
    • Topham, C. M.; Srinivasan, N.; Blundell, T. L. Prediction of the Stability of Protein Mutants Based on Structural Environment-Dependent Amino Acid Substitution and Propensity Tables Protein Eng. 1997, 10, 7-21
    • (1997) Protein Eng. , vol.10 , pp. 7-21
    • Topham, C.M.1    Srinivasan, N.2    Blundell, T.L.3
  • 47
    • 32044475396 scopus 로고    scopus 로고
    • Variable Metallation of Human Superoxide Dismutase: Atomic Resolution Crystal Structures of Cu-Zn, Zn-Zn and As-Isolated Wild-Type Enzymes
    • Strange, R. W.; Antonyuk, S. V.; Hough, M. A.; Doucette, P. A.; Valentine, J. S.; Hasnain, S. S. Variable Metallation of Human Superoxide Dismutase: Atomic Resolution Crystal Structures of Cu-Zn, Zn-Zn and As-Isolated Wild-Type Enzymes J. Mol. Biol. 2006, 356, 1152-1162
    • (2006) J. Mol. Biol. , vol.356 , pp. 1152-1162
    • Strange, R.W.1    Antonyuk, S.V.2    Hough, M.A.3    Doucette, P.A.4    Valentine, J.S.5    Hasnain, S.S.6
  • 48
    • 34547165170 scopus 로고    scopus 로고
    • Molecular Dynamics using Atomic-Resolution Structure Reveal Structural Fluctuations that may Lead to Polymerization of Human Cu-Zn Superoxide Dismutase
    • Strange, R. W.; Yong, C. W.; Smith, W.; Hasnain, S. S. Molecular Dynamics using Atomic-Resolution Structure Reveal Structural Fluctuations that may Lead to Polymerization of Human Cu-Zn Superoxide Dismutase Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 10040-10044
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 10040-10044
    • Strange, R.W.1    Yong, C.W.2    Smith, W.3    Hasnain, S.S.4
  • 50
    • 0037427449 scopus 로고    scopus 로고
    • The Structure of Holo and Metal-Deficient Wild-Type Human Cu, Zn Superoxide Dismutase and its Relevance to Familial Amyotrophic Lateral Sclerosis
    • Strange, R. W.; Antonyuk, S.; Hough, M. A.; Doucette, P. A.; Rodriguez, J. A.; Hart, P. J.; Hayward, L. J.; Valentine, J. S.; Hasnain, S. S. The Structure of Holo and Metal-Deficient Wild-Type Human Cu, Zn Superoxide Dismutase and its Relevance to Familial Amyotrophic Lateral Sclerosis J. Mol. Biol. 2003, 328, 877-891
    • (2003) J. Mol. Biol. , vol.328 , pp. 877-891
    • Strange, R.W.1    Antonyuk, S.2    Hough, M.A.3    Doucette, P.A.4    Rodriguez, J.A.5    Hart, P.J.6    Hayward, L.J.7    Valentine, J.S.8    Hasnain, S.S.9
  • 51
    • 84876917870 scopus 로고    scopus 로고
    • Stability Mechanisms of a Thermophilic Laccase Probed by Molecular Dynamics
    • Christensen, N. J.; Kepp, K. P. Stability Mechanisms of a Thermophilic Laccase Probed by Molecular Dynamics PloS ONE 2013, 8, e61985
    • (2013) PloS ONE , vol.8 , pp. 61985
    • Christensen, N.J.1    Kepp, K.P.2


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